Rational Strategy for Designing Peptidomimetic Small Molecules Based on Cyclic Peptides Targeting Protein–Protein Interaction between CTLA-4 and B7-1

Abstract

Currently, various pharmaceutical modalities are being developed rapidly. Targeting protein–protein interactions (PPIs) is an important objective in such development. Cyclic peptides, because they have good specificity and activity, have been attracting much attention as an alternative to antibody drugs. However, cyclic peptides involve some difficulties, such as oral availability and cell permeability. Therefore, while small-molecule drugs still present many benefits, the screening of functional small-molecule compounds targeting PPIs requires a great deal of time and effort, including structural analysis of targets and hits. In this study, we investigated a rational two-step strategy to design small-molecule compounds targeting PPIs. First, we obtained inhibitory cyclic peptides that bind to cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) by ribosomal display using PUREfrex® (PUREfrex®RD) to get structure–activity relation (SAR) information. Based on that information, we converted cyclic peptides to small molecules using PepMetics® scaffolds that can mimic the α-helix or β-turn of the peptide. Finally, we succeeded in generating small-molecule compounds with good IC50 (single-digit μM values) against CTLA-4. This strategy is expected to be a useful approach for small-molecule design targeting PPIs, even without having structural information such as that associated with X-ray crystal structures.

Strategies for converting turn-motif and cyclic peptides to small molecules for targeting protein–protein interactions

“…5 ). 20 Competitive ELISA was performed on 3 and peptide 1 to confirm 3 binds to CTLA-4 on the same binding surface as 1. The arrangement of the benzyl, cyclohexyl and arginyl side chains in 3 are predicted to mimic the β-turn arrangement of V10, H11 and F12 in the original peptide.…”

“…18,19 Although peptides have opened an avenue into targeting and inhibiting PPI's, small molecules are still the leading compounds found on the drug market. 20 The development of small molecules to target PPIs remains a critical task. Most small molecule design approaches tend to be focused on structure activity relationships (SAR), of large libraries of compounds based on computational modelling and refining the structures until optimum affinity is achieved.…”